protein

Gene Prediction using MAKER, CEGMA, SNAP, GENEMARK & AUGUSTUS

Shell script to prepare protein PDBs for GROMACS molecular dynamics simulations, with SLURM script included to run md with hpc

This project contains the setup and maintenance scripts for a high-performance, CUDA-accelerated protein folding environment using GROMACS and NCBI tools.

Ancestral Gene/Protein Prediction

Coiled-coil Crick Paramaterization PDB modifier for further design

Convert PDBX/mmCIF Protein Structures to PNG Images using Shell Script and Jmol.

Reads protein functional associations (e.g. from STRING-DB) and finds direct (0-hops) or indirect (1,2-hops) protein-links between a pair of proteins (C/C++).This work was done while working at the Institute of Cancer Research in London in association with people from the Erler Lab.

Protein Structure QM 2019

Computational pipeline for measuring protein interior reprogrammability. Identifies chassis candidates where exterior fold is preserved while interior chemistry varies.

Linux shell toolkit for automating common bioinformatics sequence and protein analysis tasks.

Linux shell toolkit for protein structure retrieval, sequence analysis, and PDB file processing.